merge

Merge branch 'master' of https://github.com/16EAGLE/odc_box

# Conflicts:
#	Dockerfile

Dockerfile

@@ -0,0 +1,88 @@
+FROM ubuntu:focal
+FROM opendatacube/geobase:wheels-3.0.4  as env_builder
+ARG py_env_path=/env
+
+# set rpy2 to ABI mode, since R is installed after rpy2
+ENV RPY2_CFFI_MODE=ABI
+
+# install required python libraries
+RUN mkdir -p /conf
+COPY requirements.txt /conf/
+RUN env-build-tool new /conf/requirements.txt ${py_env_path} /wheels
+
+# install ODC
+FROM opendatacube/geobase:runner-3.0.4
+ARG py_env_path=/env
+
+COPY --chown=1000:100 --from=env_builder $py_env_path $py_env_path
+COPY --from=env_builder /bin/tini /bin/tini
+
+RUN export GDAL_DATA=$(gdal-config --datadir)
+ENV LC_ALL=C.UTF-8 \
+    PATH="/env/bin:$PATH"
+
+RUN useradd -m -s /bin/bash -N jovyan -g 100 -u 1000 \
+	&& chown jovyan /home/jovyan \
+	&& addgroup jovyan staff
+
+# install R dependencies
+RUN apt-get update \
+	&& apt-get install -y --no-install-recommends \
+		software-properties-common \
+                dirmngr \
+                ed \
+		less \
+		locales \
+		vim-tiny \
+		wget \
+		ca-certificates \
+        && add-apt-repository --enable-source --yes "ppa:marutter/rrutter4.0" \
+        && add-apt-repository --enable-source --yes "ppa:c2d4u.team/c2d4u4.0+"
+
+# configure default locale, see https://github.com/rocker-org/rocker/issues/19
+RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
+	&& locale-gen en_US.utf8 \
+	&& /usr/sbin/update-locale LANG=en_US.UTF-8
+
+# set env variables for noninteractive
+ENV LC_ALL en_US.UTF-8
+ENV LANG en_US.UTF-8
+ENV TZ UTC
+
+# install R and littler, and create a link for littler in /usr/local/bin
+# Default CRAN repo is now set by R itself, and littler knows about it too
+# r-cran-docopt is not currently in c2d4u so we install from source
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update \
+        && apt-get install -y --no-install-recommends \
+                 littler \
+ 		 r-base \
+ 		 r-base-dev \
+ 		 r-recommended \
+  	&& ln -s /usr/lib/R/site-library/littler/examples/install.r /usr/local/bin/install.r \
+ 	&& ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r \
+ 	&& ln -s /usr/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
+ 	&& ln -s /usr/lib/R/site-library/littler/examples/testInstalled.r /usr/local/bin/testInstalled.r \
+ 	&& install.r docopt \
+ 	&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
+ 	&& rm -rf /var/lib/apt/lists/*
+
+# install system dependencies for suite of spatial R packages
+ARG DEBIAN_FRONTEND=noninteractive
+RUN apt-get update&&apt-get install -y apt-utils pkg-config
+RUN apt-get install -y libsqlite3-dev libudunits2-dev libssl-dev libmagick++-dev libcurl4-openssl-dev
+RUN apt-get update&&apt-get install -y --no-install-recommends r-cran-reticulate
+
+# install R packages
+RUN R -e 'install.packages(c("IRkernel", "rgdal", "sp", "raster", "sf", "basemaps", "ggplot2", "mapview", "mapedit", "devtools", "usethis", "testthat", "roxygen2"))'
+
+# initiliaze R kernel for Jupyter
+RUN R -e "IRkernel::installspec(user = FALSE)"
+
+# set user and working dir
+USER jovyan
+WORKDIR /notebooks
+
+ENTRYPOINT ["/bin/tini", "--"]
+
+CMD ["jupyter", "notebook", "--allow-root", "--ip='0.0.0.0'" "--NotebookApp.token='secretpassword'"]